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I-TASSER results for job id Rv1375

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)
 Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)


 Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)


  Ligand binding sites

Rank C-score Cluster
size
PDB
Hit
Lig
Name
Download
Complex
Ligand Binding Site Residues
10.20 12 4q85B APC Rep, Mult 71,117,126,127,130,131,134,222,223,225,229,233,237,241,322,326
20.07 4 4q85A MG Rep, Mult 117,240,241,322,326
30.04 3 4q85A MG Rep, Mult 134,221,237
40.03 2 1ofdA F3S Rep, Mult 394,399,400,402,403,422,424
50.03 2 1sijA FES Rep, Mult 116,119,122,124
60.03 2 3fahA GOL Rep, Mult 274,277,278,279,281
70.03 2 3kziX CLA Rep, Mult 221,224
80.03 2 1lm1A F3S Rep, Mult 244,246,247,252,254,285,294,295
90.02 1 4v1uA CA Rep, Mult 117,326
100.01 1 2xvaB ZN Rep, Mult 242,243
110.01 1 3phxA ZN Rep, Mult 313,315
120.01 1 3d1lB MPR Rep, Mult 153,219,220
130.01 1 3b2xA NA Rep, Mult 274,275,276,277,279
140.01 1 1zzhB ZN Rep, Mult 131,134
150.01 1 3lw52 CLA Rep, Mult 194,326
160.01 1 2e69A SO4 Rep, Mult 285,329
170.01 1 3gxqB NUC Rep, Mult 233,235

Download the all possible binding ligands and detailed prediction summary.
Download the templates clustering results.
(a)C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)Cluster size is the total number of templates in a cluster.
(c)Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster.

  Enzyme Commission (EC) numbers and active sites

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0603c46B0.3717.300.0230.6262.7.7.6322
20.0601i8qA0.3417.330.0360.5794.2.2.1391
30.0602vncB0.3316.860.0340.5333.2.1.-NA
40.0603ebgA0.3307.300.0350.5533.4.11.-NA
50.0601g5aA0.3377.210.0470.5532.4.1.4NA
60.0603k1dA0.3367.230.0270.5602.4.1.18128
70.0601dgjA0.3877.270.0420.6541.2.-.-326
80.0601t3tA0.3707.470.0520.6336.3.5.3NA
90.0601f1sA0.3387.310.0340.5674.2.2.1140
100.0601bglA0.3457.240.0490.5833.2.1.23240
110.0603fr8B0.3386.930.0450.5331.1.1.86131
120.0601ofdA0.3597.010.0400.5831.4.7.1NA
130.0602j5wA0.3387.630.0270.5851.16.3.1NA
140.0603btaA0.3337.390.0250.5703.4.24.69NA
150.0601s46A0.3357.110.0470.5472.4.1.4NA
160.0602rnpC0.3127.490.0140.5402.7.7.6NA
170.0602vdcF0.3657.200.0370.6011.4.1.13NA
180.0602vdcA0.3656.880.0410.5811.4.1.13NA
190.0601vlbA0.3937.220.0740.6581.2.99.7242

(a)CscoreEC is the confidence score for the EC number prediction. CscoreEC values range in between [0-1];
where a higher score indicates a more reliable EC number prediction.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided
by length of the query protein.

  Gene Ontology (GO) terms

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.370.7861.690.170.824q86B GO:0000287 GO:0005829 GO:0018339 GO:0047693
10.300.7474.190.180.904v1tB GO:0000166 GO:0046872
20.280.6834.310.170.834bs9A GO:0046872
30.060.3877.270.040.651dgjA GO:0009055 GO:0016491 GO:0046872 GO:0051536 GO:0051537 GO:0055114
40.060.3747.420.040.641fo4A GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0016903 GO:0043546 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
50.060.2987.710.050.524uhxA GO:0003824 GO:0004031 GO:0004854 GO:0005506 GO:0005737 GO:0005829 GO:0006954 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0042816 GO:0043546 GO:0046872 GO:0050660 GO:0051287 GO:0051536 GO:0051537 GO:0055114 GO:0070062 GO:0072593
60.060.3367.300.030.573ax7A GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0016903 GO:0043546 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
70.060.2828.180.060.531t3qB GO:0016491 GO:0055114
80.060.3168.060.040.582e1qA GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213
90.060.3637.550.040.643zyvB GO:0003824 GO:0004031 GO:0004854 GO:0005506 GO:0005737 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0030151 GO:0046872 GO:0050660 GO:0051287 GO:0051536 GO:0051537 GO:0055114
100.060.3027.620.050.531jroB GO:0016491 GO:0030151 GO:0046872 GO:0055114
110.060.3006.980.050.492fj0A GO:0016787
120.060.3027.630.050.531rm6A GO:0016491 GO:0018525 GO:0055114
130.060.2877.430.030.491n63B GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
140.060.3957.330.080.673fahA GO:0009055 GO:0016491 GO:0033727 GO:0046872 GO:0051536 GO:0051537 GO:0055114
150.060.2927.640.040.521ffuB GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
160.060.2937.510.040.514zohA GO:0016491 GO:0055114
170.060.2597.080.050.421jroA GO:0000166 GO:0003824 GO:0004854 GO:0004855 GO:0009055 GO:0016491 GO:0016614 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
180.060.3087.470.060.522ckjA GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213


Consensus prediction of GO terms
 
Molecular Function GO:0000287 GO:0047693 GO:0000166
GO-Score 0.37 0.37 0.30
Biological Processes GO:0018339
GO-Score 0.37
Cellular Component GO:0005829
GO-Score 0.41

(a)CscoreGO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on CscoreGO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]



Please cite the following articles when you use the I-TASSER server:
1. J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2. J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.